#NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Generated on April 26, 2024; 9:17 GMT TreeBASE (cc) 1994-2008 Study reference: Barker F.K. 2014. Mitogenomic data resolve basal relationships among passeriform and passeridan birds. Molecular Phylogenetics and Evolution, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S15907] BEGIN TAXA; TITLE 'Passerines with complete or near-complete mitogenomes'; DIMENSIONS NTAX=125; TAXLABELS Acanthisitta_chloris_AY325307 Acridotheres_cristatellus_NC_015613 Acrocephalus_scirpaceus_NC_010227 Agelaius_phoeniceus Agelaius_phoeniceus_JX516062 Alauda_arvensis_NC_020425 Amblyramphus_holosericeus_JX516063 Bombycilla_cedrorum Bucanetes_mongolicus Campylorhynchus_zonatus_KF509924 Cardinalis_cardinalis Carduelis_pinus Carduelis_psaltria Carduelis_sinica Carduelis_sinica_NC_015196 Carduelis_spinus_NC_015198 Carpodacus_cassinii Carpodacus_erythrinus Carpodacus_mexicanus Carpodacus_roseus Chlorophanes_spiza Chrysomus_cyanopus_JX516076 Chrysomus_icterocephalus_JX516060 Chrysomus_ruficapillus_JX516056 Chrysomus_thilius_JX516069 Chrysomus_xanthophthalmus_JX516059 Cnemotriccus_fuscatus_NC_007975 Coccothraustes_coccothraustes Coccothraustes_vespertinus Corvus_frugilegus_NC_002069 Curaeus_curaeus_JX516070 Cyanopica_cyanus_NC_015824 Cyanoptila_cyanomelana_NC_015232 Dives_dives_JX516061 Emberiza_chrysophrys_NC_015233 Emberiza_tristrami_NC_015234 Eopsaltria_australis_NC_019665 Epthianura_albifrons_NC_019664 Euphagus_cyanocephalus_JX516072 Ficedula_zanthopygia_NC_015802 Fringilla_coelebs Garrulax_canorus_NC_020429 Garrulus_glandarius_NC_015810 Gnorimopsar_chopi_JX516055 Gracula_religiosa_NC_015898 Gymnomystax_mexicanus_JX516075 Hemignathus_flavus Hemignathus_stejnegeri Hemignathus_virens Hemignathus_virens_wilsoni Himatione_sanguinea Hyliota_flavigaster Icterus_mesomelas_JX516068 Lampropsar_tanagrinus_JX516057 Lanius_tephronotus_JX486029 Leiothrix_argentauris_NC_015114 Leiothrix_lutea_NC_020427 Lepidothrix_coronata Leucosticte_arctoa Leucosticte_brandti Loxia_curvirostra Loxops_caeruleirostris Luscinia_calliope_NC_015074 Macroagelaius_imthurni_JX516073 Magumma_parva Malurus_melanocephalus Melamprosops_phaeosoma Menura_novaehollandiae_NC_007883 Molothrus_aeneus_JX516067 Molothrus_badius_JX516074 Nesopsar_nigerrimus_JX516054 Notiomystis_cincta Nucifraga_columbiana_KF509923 Oedistoma_iliolophum Oreomystis_bairdi Oreomystis_mana Oreopsar_bolivianus_JX516058 Oriolus_chinensis_NC_020424 Paroreomyza_montana Passer_domesticus Petroica_boodang_NC_019666 Petroica_goodenovii_NC_019667 Petroica_phoenicea_NC_019668 Pica_pica_NC_015200 Picathartes_gymnocephalus Pinicola_enucleator Podoces_hendersoni_NC_014879 Poecile_atricapilla Pseudoleistes_guirahuro_JX516071 Pseudoleistes_virescens_JX516066 Pseudonestor_xanthophrys Pseudopodoces_humilis_NC_014341 Pycnonotus_sinensis_NC_013838 Pycnonotus_taivanus_NC_013483 Pyrrhula_pyrrhula Regulus_calendula Scytalopus_magellanicus Serinus_albogularis Serinus_canaria Serinus_serinus Sitta_carolinensis Smithornis_sharpei_NC_000879 Sturnus_cineraceus_NC_015237 Sturnus_nigricollis_NC_020423 Sturnus_sericeus_NC_014455 Sturnus_tristis_NC_015195 Sylvia_atricapilla_NC_010228 Sylvia_crassirostris_NC_010229 Tachycineta_albilinea_NC_020601 Tachycineta_albiventer_NC_020602 Tachycineta_bicolor_NC_020596 Tachycineta_euchrysea_NC_020598 Tachycineta_leucorrhoa_NC_020603 Tachycineta_stolzmanni_NC_020600 Taeniopygia_guttata_NC_007897 Thamnophilus_nigrocinereus Thraupis_episcopus Tregellasia_leucops Turdus_migratorius Uragus_sibiricus Urocissa_erythrorhyncha_NC_020426 Vestiaria_coccinea Vidua_chalybeata_NC_000880 Vireo_olivaceus Xanthopsar_flavus_JX516065 ; END; BEGIN TREES; TITLE 'RAxML Result for Analysis with Partitionfinder Partitioning + AGY Coding'; LINK TAXA = 'Passerines with complete or near-complete mitogenomes'; TREE pfinder_AGY = [&R] (Acanthisitta_chloris_AY325307:0.2064172806560685,((Smithornis_sharpei_NC_000879:0.5227902530303447,((Cnemotriccus_fuscatus_NC_007975:0.2636749766698192,Lepidothrix_coronata:0.21773601017681243):0.11678568125312117,(Scytalopus_magellanicus:0.28608106244169285,Thamnophilus_nigrocinereus:0.2766441778914659):0.0662428844015015):0.03429325794222271):0.06996860481046763,(Menura_novaehollandiae_NC_007883:0.2848012302617067,((Epthianura_albifrons_NC_019664:0.26563782306254047,Malurus_melanocephalus:0.203772826317274):0.04268627854400919,(((Oriolus_chinensis_NC_020424:0.23079233498397367,Vireo_olivaceus:0.23870338113184353):0.035502546325485884,(Lanius_tephronotus_JX486029:0.22122870533564265,(Urocissa_erythrorhyncha_NC_020426:0.1049037099567286,(Cyanopica_cyanus_NC_015824:0.12355327355193235,((Podoces_hendersoni_NC_014879:0.0994355470412931,Pica_pica_NC_015200:0.07540022291631798):0.008830166296741382,(Garrulus_glandarius_NC_015810:0.07687278079521909,(Nucifraga_columbiana_KF509923:0.05844381694381873,Corvus_frugilegus_NC_002069:0.06956519962033036):0.019337689764321042):0.006425940892418436):0.012725480991095162):0.008740649829901193):0.06460046083203586):0.053564346398596974):0.039837111588897134,(Oedistoma_iliolophum:0.23850147519670084,((Notiomystis_cincta:0.33850335901321527,((Tregellasia_leucops:0.06573967147976567,Eopsaltria_australis_NC_019665:0.07337535020387154):0.15463949928057608,(Petroica_goodenovii_NC_019667:0.036014758870712704,(Petroica_phoenicea_NC_019668:0.02043313269914615,Petroica_boodang_NC_019666:0.02685278453922557):0.026389278146181527):0.142385301536625):0.023670766567227663):0.015676778371970346,(Picathartes_gymnocephalus:0.34844007169568336,(((Hyliota_flavigaster:0.2445825117615117,Poecile_atricapilla:0.17434207574665506):0.018219810652264745,(Alauda_arvensis_NC_020425:0.26817172633362485,(Acrocephalus_scirpaceus_NC_010227:0.20085907025832106,(((Sylvia_atricapilla_NC_010228:0.16673713316664318,Sylvia_crassirostris_NC_010229:0.14144747871688912):0.08575503308438359,(Garrulax_canorus_NC_020429:0.13757488249287453,(Leiothrix_lutea_NC_020427:0.024313837353510892,Leiothrix_argentauris_NC_015114:0.03606786567219766):0.09805720000097184):0.09102393523581576):0.021137456027545354,((Pycnonotus_sinensis_NC_013838:3.580312066157054E-4,Pycnonotus_taivanus_NC_013483:0.001636509984966339):0.20004227094783544,((Tachycineta_bicolor_NC_020596:0.04982110107870852,Tachycineta_euchrysea_NC_020598:0.041757409004085644):0.011720328182968975,(Tachycineta_leucorrhoa_NC_020603:0.026188880312565277,(Tachycineta_stolzmanni_NC_020600:0.026707593944544472,(Tachycineta_albilinea_NC_020601:0.009038321314973508,Tachycineta_albiventer_NC_020602:0.012060084589651576):0.01533200084459807):0.011724150935044197):0.01258902515875926):0.2505256221436425):0.016185637306016076):0.00817615262557636):0.021748355578738):0.014065411409288076):0.013912780800778846,(((Campylorhynchus_zonatus_KF509924:0.27696291068048184,Sitta_carolinensis:0.27147225781006123):0.030994287067640736,((Turdus_migratorius:0.16629101056435747,(Cyanoptila_cyanomelana_NC_015232:0.11192630375791324,(Ficedula_zanthopygia_NC_015802:0.09620461987775131,(Luscinia_calliope_NC_015074:0.08272720198404515,Pseudopodoces_humilis_NC_014341:0.10628798120557847):0.007583469419917832):0.01353563248895906):0.049189861488610154):0.013866008809195196,(Gracula_religiosa_NC_015898:0.10117193361076104,(Sturnus_nigricollis_NC_020423:0.061967624075728645,((Acridotheres_cristatellus_NC_015613:0.01890446768335763,Sturnus_tristis_NC_015195:0.01685100220576885):0.011329291250478324,(Sturnus_cineraceus_NC_015237:0.035821705478464416,Sturnus_sericeus_NC_014455:0.03575714464378987):0.004367077855561785):0.013885298911715305):0.10392784089082352):0.04515771939469204):0.05317441479743901):0.009523915895686574,((Regulus_calendula:0.2898737455842826,Bombycilla_cedrorum:0.2417013973595331):0.017255453688175493,((Taeniopygia_guttata_NC_007897:0.1182361270354022,Vidua_chalybeata_NC_000880:0.2032191612961063):0.05353190365648719,(Passer_domesticus:0.1678695188056174,(((Cardinalis_cardinalis:0.08837993136545519,(Thraupis_episcopus:0.07478050660047364,Chlorophanes_spiza:0.08052532669699075):0.010730574736317111):0.006921265850310054,((Emberiza_tristrami_NC_015234:0.024167342286922855,Emberiza_chrysophrys_NC_015233:0.025795200081875747):0.07521719847867903,(Icterus_mesomelas_JX516068:0.052682741841657,((Molothrus_aeneus_JX516067:0.04163279513484519,(Agelaius_phoeniceus_JX516062:1.1526365501168812E-5,Agelaius_phoeniceus:0.0017650963766299155):0.038935961154033194):0.002611285756742854,(Nesopsar_nigerrimus_JX516054:0.038916537719145716,((Dives_dives_JX516061:0.039662959533016684,Euphagus_cyanocephalus_JX516072:0.032020990294270635):0.004740294457944327,((Macroagelaius_imthurni_JX516073:0.047570314436419014,(Gymnomystax_mexicanus_JX516075:0.03806334451013038,Lampropsar_tanagrinus_JX516057:0.02627830146146448):0.0037590852710245315):0.002367460185557446,((Curaeus_curaeus_JX516070:0.026233257784594066,Amblyramphus_holosericeus_JX516063:0.032037253097306984):0.008329960853016405,(Gnorimopsar_chopi_JX516055:0.034478713543180106,((Molothrus_badius_JX516074:0.01797205535231028,Oreopsar_bolivianus_JX516058:0.02079834531756608):0.00840280368962465,((Chrysomus_thilius_JX516069:0.0240999652483902,(Chrysomus_xanthophthalmus_JX516059:9.822966949286638E-4,Chrysomus_cyanopus_JX516076:0.0011985941306542625):0.022933748535927334):0.006119898617156672,((Chrysomus_ruficapillus_JX516056:0.004593916629809791,Chrysomus_icterocephalus_JX516060:0.006629522305144686):0.019082608431151726,(Xanthopsar_flavus_JX516065:0.007675688766144884,(Pseudoleistes_guirahuro_JX516071:0.0074195787070930885,Pseudoleistes_virescens_JX516066:0.007032649943769398):0.005626461513011605):0.011629042647542054):0.004119035354454237):0.0012449746355434055):6.403707917835844E-4):0.0032547414272194874):0.002659767679311975):0.009245091362173663):0.004272457659350359):0.0020230235060394453):0.024606030454618844):0.023869758172376354):0.010109836390896021):0.03357314703061398,(Fringilla_coelebs:0.13252421231241596,((Coccothraustes_coccothraustes:0.054047801052158784,Coccothraustes_vespertinus:0.056460761454535935):0.06408820426491035,(((Carpodacus_cassinii:0.062454372756790444,Carpodacus_mexicanus:0.07622871260683028):0.013554908598860327,((Carduelis_sinica_NC_015196:5.100840703897713E-4,Carduelis_sinica:7.267847734117039E-4):0.037467445580781744,((Serinus_albogularis:0.028079358485272654,Serinus_serinus:0.03306210565813639):0.00735796273519107,(Loxia_curvirostra:0.03461103631473372,(Serinus_canaria:0.018011166477891916,(Carduelis_psaltria:0.01716645925048721,(Carduelis_pinus:0.00679285680555719,Carduelis_spinus_NC_015198:0.006904366898946135):0.006683284506650677):0.006291180705366273):0.0059482295531958496):0.0025285687819782687):0.004336010072247376):0.030181134217751593):0.017387901160814345,(((Pinicola_enucleator:0.07188371750789302,Pyrrhula_pyrrhula:0.06440123066029368):0.02929076870551639,(Bucanetes_mongolicus:0.08251618654670478,(Leucosticte_arctoa:0.012382211413344169,Leucosticte_brandti:0.010377423195229274):0.06337585911313315):0.012562648234460738):0.003321710207631723,((Carpodacus_erythrinus:0.06261910433569506,(Carpodacus_roseus:0.032684231875326986,Uragus_sibiricus:0.04497359810893309):0.028577724562491635):0.010876829710737002,(Melamprosops_phaeosoma:0.04935317991629651,((Paroreomyza_montana:0.036703797883633094,Oreomystis_bairdi:0.043943940581317564):0.005250041356555379,((Himatione_sanguinea:0.015937552186360504,Vestiaria_coccinea:0.012695644007040263):0.013085308754706815,((Magumma_parva:0.02173894015100919,Pseudonestor_xanthophrys:0.031172140164885453):0.0019555246949533034,((Oreomystis_mana:0.014793692746988052,Loxops_caeruleirostris:0.013745051143965403):0.0031899415439604617,((Hemignathus_virens_wilsoni:0.0023313453408351226,Hemignathus_virens:0.0036283224134894265):0.009952733756824594,(Hemignathus_flavus:0.011747217513355945,Hemignathus_stejnegeri:0.013144479280485122):0.0020695841072595478):0.006745532323487069):0.0023681095695763377):0.005125202171036625):0.016942660994023084):0.011660426285000303):0.034342834196761984):0.004690882459245094):0.004229994050945929):0.03936915110042938):0.02119702739795426):0.018237825497762317):0.028932353198030003):0.02294812342765784):0.05692123181676079):0.005789395429379396):0.011777188148215822):0.014880641602441513):0.00998753583190315):0.008355759660517381):0.01329836064104295):0.04155592109381523):0.07910735533066338):0.21394477723315708):0.2064172806560685); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr77157] END;